Variant report
| Variant | rs7550884 |
|---|---|
| Chromosome Location | chr1:220459596-220459597 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:4)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:4 , 50 per page) page:
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr1:220437133..220439238-chr1:220458442..220459950,2 | K562 | blood: | |
| 2 | chr1:220448590..220453578-chr1:220456317..220461314,5 | K562 | blood: | |
| 3 | chr1:220453040..220456116-chr1:220457163..220460611,3 | K562 | blood: | |
| 4 | chr1:220443856..220448650-chr1:220458115..220462715,5 | K562 | blood: |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000118873 | Chromatin interaction |
rSNPs within LD-proxies of this variant (count:13)
| rs_ID | r2[population] |
|---|---|
| rs12080669 | 0.81[AMR][1000 genomes];0.81[EUR][1000 genomes] |
| rs55874043 | 1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs60326603 | 1.00[AMR][1000 genomes];0.94[EUR][1000 genomes] |
| rs73092160 | 0.90[AMR][1000 genomes];0.85[EUR][1000 genomes] |
| rs73095644 | 1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs73101290 | 0.90[AMR][1000 genomes];0.81[EUR][1000 genomes] |
| rs73102536 | 1.00[AMR][1000 genomes];0.94[EUR][1000 genomes] |
| rs73103010 | 0.90[AMR][1000 genomes];0.81[EUR][1000 genomes] |
| rs73103020 | 1.00[AMR][1000 genomes];0.81[EUR][1000 genomes] |
| rs73103022 | 1.00[AMR][1000 genomes];0.81[EUR][1000 genomes] |
| rs73103033 | 0.81[AMR][1000 genomes] |
| rs73104956 | 0.81[AMR][1000 genomes] |
| rs7526504 | 1.00[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page:
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| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1001681 | chr1:220425057-220548325 | Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 9 gene(s) | inside rSNPs | diseases |
| 2 | nsv535298 | chr1:220425057-220548325 | Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 9 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:2)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs7550884 | ACSM3 | trans | lymphoblastoid | seeQTL |
| rs7550884 | TGFBR3 | trans | lymphoblastoid | seeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:220457600-220463600 | Weak transcription | Cortex derived primary cultured neurospheres | brain |
